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- PDB-8hpd: Bry-LHCII heterotrimer of Bryopsis corticulans -

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Basic information

Entry
Database: PDB / ID: 8hpd
TitleBry-LHCII heterotrimer of Bryopsis corticulans
Components(siphonaxanthin chlorophyll a/b binding light-harvesting complex II, Bry- ...) x 3
KeywordsPHOTOSYNTHESIS / Light-harvesting complexes / siphonaxanthin / siphonein
Function / homology
Function and homology information


Chlorophyll a-b binding protein / Chlorophyll a/b binding protein domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Siphonaxanthin / Siphonein / CHLOROPHYLL B / CHLOROPHYLL A / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Chem-NEX
Similarity search - Component
Biological speciesBryopsis corticulans (plant)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.74 Å
AuthorsLi, Z.H. / Shen, J.R. / Wang, W.D.
Funding support China, 9items
OrganizationGrant numberCountry
Chinese Academy of Sciences2019YFA0906300 China
Chinese Academy of Sciences2021YFA1300403 China
Chinese Academy of SciencesXDA26050402 China
Chinese Academy of SciencesXDB17000000 China
Chinese Academy of Sciences2020081 China
Chinese Academy of SciencesJCTD-2020-06 China
Chinese Academy of SciencesYSBR-004 China
Chinese Academy of Sciences31970260 China
Chinese Academy of Sciences32222007 China
CitationJournal: Structure / Year: 2023
Title: Structural and functional properties of different types of siphonous LHCII trimers from an intertidal green alga Bryopsis corticulans.
Authors: Zhenhua Li / Cuicui Zhou / Songhao Zhao / Jinyang Zhang / Xueyang Liu / Min Sang / Xiaochun Qin / Yanyan Yang / Guangye Han / Tingyun Kuang / Jian-Ren Shen / Wenda Wang /
Abstract: Light-harvesting complexes of photosystem II (LHCIIs) in green algae and plants are vital antenna apparatus for light harvesting, energy transfer, and photoprotection. Here we determined the ...Light-harvesting complexes of photosystem II (LHCIIs) in green algae and plants are vital antenna apparatus for light harvesting, energy transfer, and photoprotection. Here we determined the structure of a siphonous-type LHCII trimer from the intertidal green alga Bryopsis corticulans by X-ray crystallography and cryo-electron microscopy (cryo-EM), and analyzed its functional properties by spectral analysis. The Bryopsis LHCII (Bry-LHCII) structures in both homotrimeric and heterotrimeric form show that green light-absorbing siphonaxanthin and siphonein occupied the sites of lutein and violaxanthin in plant LHCII, and two extra chlorophylls (Chls) b replaced Chls a. Binding of these pigments expands the blue-green light absorption of B. corticulans in the tidal zone. We observed differences between the Bry-LHCII homotrimer crystal and cryo-EM structures, and also between Bry-LHCII homotrimer and heterotrimer cryo-EM structures. These conformational changes may reflect the flexibility of Bry-LHCII, which may be required to adapt to light fluctuations from tidal rhythms.
History
DepositionDec 12, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 6, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: siphonaxanthin chlorophyll a/b binding light-harvesting complex II, Bry-Lhcb1
B: siphonaxanthin chlorophyll a/b binding light-harvesting complex II, Bry-Lhcb3
C: siphonaxanthin chlorophyll a/b binding light-harvesting complex II, Bry-Lhcb2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,09859
Polymers81,9173
Non-polymers47,18156
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Siphonaxanthin chlorophyll a/b binding light-harvesting complex II, Bry- ... , 3 types, 3 molecules ABC

#1: Protein siphonaxanthin chlorophyll a/b binding light-harvesting complex II, Bry-Lhcb1


Mass: 26696.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant)
#2: Protein siphonaxanthin chlorophyll a/b binding light-harvesting complex II, Bry-Lhcb3


Mass: 27273.939 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant)
#3: Protein siphonaxanthin chlorophyll a/b binding light-harvesting complex II, Bry-Lhcb2


Mass: 27946.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant)

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Non-polymers , 6 types, 56 molecules

#4: Chemical ChemComp-0UR / Siphonein


Mass: 781.157 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C52H76O5 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-0IE / Siphonaxanthin


Mass: 600.870 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C40H56O4
#6: Chemical ChemComp-NEX / (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY-2,2,6-TRIMETHYL-7-OXABICYCLO[4.1.0]HEPT-1-YL]-3,7,12,16-TETRAMETHYLOCTADECA-1,3,5,7,9,11,13,15,17-NONAENYLIDENE}-1,5,5-TRIMETHYLCYCLOHEXANE-1,3-DIOL / (3S,5R,6R,3'S,5'R,6'S)-5',6'-EPOXY-6,7-DIDEHYDRO- 5,6,5',6'-TETRAHYDRO-BETA,BETA-CAROTENE-3,5,3'-TRIOL / 9'-CIS-NEOXANTHIN


Mass: 600.870 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C40H56O4 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical...
ChemComp-CHL / CHLOROPHYLL B


Mass: 907.472 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C55H70MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C55H72MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C38H75O10P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Bryopsis corticulans chlorophyll a/b-type light-harvesting complex II heterotrimer
Type: COMPLEX / Entity ID: #1-#3 / Source: NATURAL
Source (natural)Organism: Bryopsis corticulans (plant)
Buffer solutionpH: 7.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.74 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1298053 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0068451
ELECTRON MICROSCOPYf_angle_d1.65111937
ELECTRON MICROSCOPYf_dihedral_angle_d13.6241778
ELECTRON MICROSCOPYf_chiral_restr0.045897
ELECTRON MICROSCOPYf_plane_restr0.0041508

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